8DNZ

Cryo-EM structure of the human Sec61 complex inhibited by apratoxin F

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Protein translocase subunit SecE-like	8098782	3002174	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	SecY-like	8098818	3000333	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	F_UNCLASSIFIED	e8dnzB1	A: extended segments	X: Preprotein translocase SecE subunit (From Topology)	H: Preprotein translocase SecE subunit (From Topology)	T: Preprotein translocase SecE subunit	F: F_UNCLASSIFIED	ECOD (1.6)
B [auth C]	F_UNCLASSIFIED	e8dnzC1	A: extended segments	X: Sec-beta subunit (From Topology)	H: Sec-beta subunit (From Topology)	T: Sec-beta subunit	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth A]	F_UNCLASSIFIED	e8dnzA1	A: alpha complex topology	X: Preprotein translocase SecY subunit (From Topology)	H: Preprotein translocase SecY subunit (From Topology)	T: Preprotein translocase SecY subunit	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF00584	SecE/Sec61-gamma subunits of protein translocation complex (SecE)	SecE/Sec61-gamma subunits of protein translocation complex	-	Family
C [auth A]	PF10559	Plug domain of Sec61p (Plug_translocon)	Plug domain of Sec61p	The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unl ...	The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unlikely to be important for sealing the translocation pore in yeast but it plays a role in stabilising Sec61p during translocon formation. The domain runs from residues 52-74 [1].	Domain
C [auth A]	PF00344	SecY (SecY)	SecY	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Protein transport protein Sec61 subunit gamma	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity ribonucleoprotein complex binding protein-containing complex binding binding ribosome binding	protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein targeting localization protein transmembrane transport cellular macromolecule localization establishment of localization in cell post-translational protein targeting to membrane, translocation establishment of protein localization to endoplasmic reticulum protein localization to endoplasmic reticulum establishment of protein localization to membrane protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein targeting localization protein transmembrane transport cellular macromolecule localization establishment of localization in cell post-translational protein targeting to membrane, translocation establishment of protein localization to endoplasmic reticulum protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport post-translational protein targeting to endoplasmic reticulum membrane localization within membrane protein localization to membrane establishment of localization protein targeting to membrane transmembrane transport establishment of protein localization to organelle protein transport macromolecule localization protein localization to organelle cellular process intracellular protein transport protein targeting to ER	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane membrane-bounded organelle protein-containing complex membrane protein complex endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane membrane-bounded organelle protein-containing complex membrane protein complex endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane Ssh1 translocon complex organelle subcompartment intracellular membrane-bounded organelle translocon complex rough endoplasmic reticulum membrane organelle endoplasmic reticulum organelle membrane
B [auth C]	Protein transport protein Sec61 subunit beta	GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity ribonucleoprotein complex binding protein-containing complex binding binding ribosome binding protein binding growth factor binding epidermal growth factor binding hormone binding RNA binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity ribonucleoprotein complex binding protein-containing complex binding binding ribosome binding protein binding growth factor binding epidermal growth factor binding hormone binding RNA binding organic cyclic compound binding nucleic acid binding	cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress proteolysis cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress proteolysis cellular process metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein targeting localization protein transmembrane transport cellular macromolecule localization establishment of localization in cell post-translational protein targeting to membrane, translocation establishment of protein localization to endoplasmic reticulum protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport post-translational protein targeting to endoplasmic reticulum membrane localization within membrane protein localization to membrane establishment of localization protein targeting to membrane transmembrane transport establishment of protein localization to organelle protein transport macromolecule localization protein localization to organelle intracellular protein transport protein targeting to ER protein exit from endoplasmic reticulum endoplasmic reticulum to cytosol transport retrograde protein transport, ER to cytosol SRP-dependent cotranslational protein targeting to membrane cotranslational protein targeting to membrane SRP-dependent cotranslational protein targeting to membrane, translocation	membrane-bounded organelle protein-containing complex intracellular anatomical structure Sec61 translocon complex membrane protein complex endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure Sec61 translocon complex membrane protein complex endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane organelle subcompartment membrane intracellular membrane-bounded organelle translocon complex rough endoplasmic reticulum membrane organelle endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum quality control compartment endoplasmic reticulum Sec complex cytosol
C [auth A]	Protein transport protein Sec61 subunit alpha isoform 1	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity signal sequence binding binding peptide binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding calcium channel activity monoatomic cation transmembrane transporter activity monoatomic ion channel activity macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity signal sequence binding binding peptide binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding calcium channel activity monoatomic cation transmembrane transporter activity monoatomic ion channel activity monoatomic cation channel activity passive transmembrane transporter activity calcium ion transmembrane transporter activity inorganic molecular entity transmembrane transporter activity channel activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity metal ion transmembrane transporter activity	cellular component organization organelle organization cellular process cellular component organization or biogenesis endoplasmic reticulum organization endomembrane system organization protein localization establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane protein localization to membrane establishment of localization cellular component organization organelle organization cellular process cellular component organization or biogenesis endoplasmic reticulum organization endomembrane system organization protein localization establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane protein localization to membrane establishment of localization protein targeting to membrane localization SRP-dependent cotranslational protein targeting to membrane establishment of protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to organelle cotranslational protein targeting to membrane establishment of protein localization to endoplasmic reticulum protein localization to endoplasmic reticulum protein targeting to ER developmental process multicellular organismal process pronephric nephron development animal organ development renal system development multicellular organism development pronephros development anatomical structure development nephron development kidney development system development membrane organization protein insertion into membrane protein insertion into ER membrane post-translational protein targeting to endoplasmic reticulum membrane nitrogen compound transport transport protein transmembrane transport establishment of localization in cell post-translational protein targeting to membrane, translocation intracellular protein transmembrane transport intracellular transport transmembrane transport protein transport intracellular protein transport SRP-dependent cotranslational protein targeting to membrane, translocation	membrane-bounded organelle protein-containing complex intracellular anatomical structure Sec61 translocon complex membrane protein complex endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure Sec61 translocon complex membrane protein complex endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane organelle subcompartment membrane intracellular membrane-bounded organelle translocon complex rough endoplasmic reticulum membrane organelle endoplasmic reticulum cytoplasm organelle membrane
D	Apratoxin F peptide inhibitor	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR008158	Protein translocase SEC61 complex, gamma subunit	Family
A [auth B]	IPR001901	Protein translocase complex, SecE/Sec61-gamma subunit	Family
A [auth B]	IPR023391	Protein translocase SecE domain superfamily	Homologous Superfamily
B [auth C]	IPR030671	Protein transport Sec61-beta/Sbh	Family
B [auth C]	IPR016482	Protein transport protein SecG/Sec61-beta/Sbh	Family
C [auth A]	IPR002208	SecY/SEC61-alpha family	Family
C [auth A]	IPR030659	SecY conserved site	Conserved Site
C [auth A]	IPR023201	SecY domain superfamily	Homologous Superfamily
C [auth A]	IPR019561	Translocon Sec61/SecY, plug domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B]	Pharos: P60059	glioblastoma brain glioma lung cancer medulloblastoma pancreatic ductal adenocarcinoma diabetes mellitus lymphoplasmacytic lymphoma osteosarcoma plasma cell myeloma malignant glioma ovarian cancer
B [auth C]	Pharos: P60468	age-related macular degeneration hepatocellular carcinoma pancreatic ductal adenocarcinoma dermatomyositis osteosarcoma psoriasis glioblastoma ovarian cancer wet macular degeneration
C [auth A]	Pharos: P61619	hyperuricemic nephropathy, familial juvenile type 4 Craniofacial Abnormalities primitive neuroectodermal tumor subependymal giant cell astrocytoma astrocytic tumor glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma prostate carcinoma tuberculosis atypical teratoid rhabdoid tumor malignant ependymoma hyperuricemic nephropathy, familial juvenile type 4 Craniofacial Abnormalities primitive neuroectodermal tumor subependymal giant cell astrocytoma astrocytic tumor glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma prostate carcinoma tuberculosis atypical teratoid rhabdoid tumor malignant ependymoma non-small cell lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia polycystic ovary syndrome psoriasis invasive ductal breast carcinoma malignant glioma oligodendroglioma pancreatic ductal adenocarcinoma pilocytic astrocytoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth B], B [auth C], C [auth A]	OPM	Transmembrane	Alpha-helical polytopic	General secretory pathway (Sec)	Protein translocase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth B], B [auth C], C [auth A]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth B], B [auth C], C [auth A]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sec, Translocase, and Insertase Proteins	Sec61 translocase, partially-open apo state (class 1)

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D	0A1	Parent Component: TYR
D	IML	Parent Component: ILE RESID: AA0336 PSI-MOD : N-methyl-L-isoleucine MOD:00341
D	MAA	Parent Component: ALA RESID: AA0336 , AA0061 PSI-MOD : N-methyl-L-isoleucine MOD:00341 , N-methyl-L-alanine MOD:00070
D	T69	RESID: AA0336 , AA0061

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.